> For the complete documentation index, see [llms.txt](https://docs.owkin.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.owkin.com/connect-and-integrate/pathology-explorer-mcp-ai-powered-tissue-analysis.md).

# Pathology Explorer: AI-powered tissue analysis

Pathology Explorer is an advanced AI tool that transforms standard hematoxylin and eosin (H\&E) histology slides into detailed, queryable insights. By analyzing the complex spatial organization of the tumor microenvironment (TME), it enables researchers to uncover patterns that traditional histology analysis often misses—patterns that are critical for predicting treatment response and understanding disease progression.

### Where to use it

Pathology Explorer is available in two places:

|                                              | In K-Pro                        | In Claude (MCP connector)                          |
| -------------------------------------------- | ------------------------------- | -------------------------------------------------- |
| Setup                                        | None: built into the K-Pro chat | Add Owkin as a custom connector (paid Claude plan) |
| Cohorts                                      | 26 TCGA cohorts and IBDColEpi   | 26 TCGA cohorts                                    |
| Thumbnails, tiles with predictions           | Yes                             | Yes                                                |
| Histomics features, survival, Parquet export | Yes                             | Yes                                                |
| Interactive whole-slide viewer               | Yes                             | No                                                 |
| Custom questions on the feature tables       | Yes                             | No                                                 |
| Guide                                        | Use Pathology Explorer in K-Pro | Use Pathology Explorer in Claude                   |

### Key Capabilities

* **Comprehensive Cell Segmentation and Classification:** Built on Owkin's HistoPLUS model, trained on more than 100,000 annotated nuclei, Pathology Explorer automatically segments and classifies cells within a tissue sample in minutes. See the [HistoPLUS paper](https://arxiv.org/abs/2508.09926).
* **Actionable Biomarker Discovery:** Transform raw histology data into interpretable, clinically relevant biomarkers that can inform research decisions and therapeutic strategies.
* **State-of-the-Art AI Architecture:** Powered by Owkin's advanced deep learning models, rigorously benchmarked against 6+ leading encoders and best-in-class architectures to ensure accuracy and reliability.
* **Large-Scale Database Integration:** Seamlessly analyze H\&E slides from major databases including The Cancer Genome Atlas (TCGA), enabling large-scale retrospective and prospective studies.

### Applications

Pathology Explorer empowers researchers and clinicians to:

* Quantify spatial relationships within the tumor microenvironment
* Identify predictive biomarkers for treatment response
* Accelerate histopathology research with automated, reproducible analysis
* Generate hypotheses about disease mechanisms based on tissue architecture


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